* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.jbappletgui;\r
\r
-import java.awt.event.*;\r
import java.awt.*;\r
-\r
-public class GAlignFrame extends Frame\r
-{\r
- protected MenuBar alignFrameMenuBar = new MenuBar();\r
- protected Menu fileMenu = new Menu();\r
- protected MenuItem closeMenuItem = new MenuItem();\r
- protected Menu editMenu = new Menu();\r
- protected Menu viewMenu = new Menu();\r
- protected Menu colourMenu = new Menu();\r
- protected Menu calculateMenu = new Menu();\r
- protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem invertSequenceMenuItem = new MenuItem();\r
- protected MenuItem remove2LeftMenuItem = new MenuItem();\r
- protected MenuItem remove2RightMenuItem = new MenuItem();\r
- protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
- protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
- protected MenuItem sortIDMenuItem = new MenuItem();\r
- protected MenuItem sortGroupMenuItem = new MenuItem();\r
- protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- protected MenuItem PCAMenuItem = new MenuItem();\r
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public Label statusBar = new Label();\r
- protected Menu outputTextboxMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem overviewMenuItem = new MenuItem();\r
- protected MenuItem undoMenuItem = new MenuItem();\r
- protected MenuItem redoMenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
- MenuItem findMenuItem = new MenuItem();\r
- Menu searchMenu = new Menu();\r
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- protected MenuItem nucleotideColour = new MenuItem();\r
- MenuItem deleteGroups = new MenuItem();\r
- MenuItem delete = new MenuItem();\r
- MenuItem copy = new MenuItem();\r
- MenuItem cut = new MenuItem();\r
- Menu Menu1 = new Menu();\r
- MenuItem pasteNew = new MenuItem();\r
- MenuItem pasteThis = new MenuItem();\r
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- protected MenuItem font = new MenuItem();\r
- protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
- MenuItem modifyPID = new MenuItem();\r
- MenuItem modifyConservation = new MenuItem();\r
- protected Menu sortByTreeMenu = new Menu();\r
- Menu sort = new Menu();\r
- Menu calculate = new Menu();\r
- MenuItem inputText = new MenuItem();\r
- Menu helpMenu = new Menu();\r
- MenuItem documentation = new MenuItem();\r
- MenuItem about = new MenuItem();\r
- public GAlignFrame()\r
- {\r
- try\r
- {\r
- jbInit();\r
- setMenuBar(alignFrameMenuBar);\r
-\r
- MenuItem item;\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- saveAs_actionPerformed(e);\r
- }\r
- });\r
-\r
- item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add( item );\r
- }\r
-\r
- }\r
- catch(Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- fileMenu.setLabel("File");\r
- closeMenuItem.setLabel("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setLabel("Edit");\r
- viewMenu.setLabel("View");\r
- colourMenu.setLabel("Colour");\r
- calculateMenu.setLabel("Calculate");\r
- selectAllSequenceMenuItem.setLabel("Select all");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setLabel("Deselect All");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setLabel("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- viewBoxesMenuItem_actionPerformed(null);\r
- }\r
- });\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- viewTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setLabel("Principal Component Analysis...");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setLabel("Average Distance Using % Identity...");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setLabel("Average Distance Using BLOSUM62...");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setState(true);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- annotationPanelMenuItem_actionPerformed(null);\r
- }\r
- });\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- colourTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- overviewMenuItem.setLabel("Overview Window...");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(null);\r
- }\r
- });\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- wrapMenuItem_actionPerformed(null);\r
- }\r
- });\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- renderGapsMenuItem_actionPerformed(null);\r
- }\r
- });\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setLabel("Search");\r
-\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- abovePIDThreshold_actionPerformed(null);\r
- }\r
- });\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setLabel("Copy");\r
- copy.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setLabel("Cut");\r
- cut.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setLabel("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- Menu1.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(new java.awt.event.ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- applyToAllGroups_actionPerformed(null);\r
- }\r
- });\r
- font.setLabel("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- font_actionPerformed(e);\r
- }\r
- });\r
- fullSeqId.setLabel("Show Full Sequence ID");\r
- fullSeqId.setState(true);\r
- fullSeqId.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- fullSeqId_actionPerformed(null);\r
- }\r
- });\r
- scaleAbove.setLabel("Scale Above");\r
- scaleAbove.setState(true);\r
- scaleAbove.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleAbove_actionPerformed(null);\r
- }\r
- });\r
- scaleLeft.setEnabled(false);\r
- scaleLeft.setState(true);\r
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleLeft_actionPerformed(null);\r
- }\r
- });\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(new java.awt.event.ItemListener()\r
- {\r
-\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
-\r
- scaleRight_actionPerformed(null);\r
- }\r
- });\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- inputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- documentation_actionPerformed(e);\r
- }\r
- });\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- about_actionPerformed(e);\r
- }\r
- });\r
-\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(helpMenu);\r
- fileMenu.add(inputText);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(Menu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
- viewMenu.add(fullSeqId);\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- this.add(statusBar, BorderLayout.SOUTH);\r
- Menu1.add(pasteNew);\r
- Menu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
-\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
+import java.awt.event.*;\r
\r
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
+public class GAlignFrame extends Frame {\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu();\r
+ protected MenuItem closeMenuItem = new MenuItem();\r
+ protected Menu editMenu = new Menu();\r
+ protected Menu viewMenu = new Menu();\r
+ protected Menu colourMenu = new Menu();\r
+ protected Menu calculateMenu = new Menu();\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem();\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ Menu searchMenu = new Menu();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu Menu1 = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+\r
+ public GAlignFrame() {\r
+ try {\r
+ jbInit();\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
+ item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ saveAs_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+ }\r
\r
- }\r
+ private void jbInit() throws Exception {\r
+ fileMenu.setLabel("File");\r
+ closeMenuItem.setLabel("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setLabel("Edit");\r
+ viewMenu.setLabel("View");\r
+ colourMenu.setLabel("Colour");\r
+ calculateMenu.setLabel("Calculate");\r
+ selectAllSequenceMenuItem.setLabel("Select all");\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setLabel("Deselect All");\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setLabel("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setLabel("Principal Component Analysis...");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity...");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity...");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62...");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62...");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setState(true);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ colourTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ overviewMenuItem.setLabel("Overview Window...");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ conservationMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ renderGapsMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setLabel("Search");\r
+\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ abovePIDThreshold_actionPerformed(null);\r
+ }\r
+ });\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ Menu1.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ applyToAllGroups_actionPerformed(null);\r
+ }\r
+ });\r
+ font.setLabel("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ fullSeqId.setLabel("Show Full Sequence ID");\r
+ fullSeqId.setState(true);\r
+ fullSeqId.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fullSeqId_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleAbove_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleLeft_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleRight_actionPerformed(null);\r
+ }\r
+ });\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ documentation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ about_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(Menu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(fullSeqId);\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ Menu1.add(pasteNew);\r
+ Menu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ }\r
\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void saveAs_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void outputText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void printMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
- {\r
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void copy_actionPerformed(ActionEvent e)\r
- {\r
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
- {\r
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
- {\r
+ protected void clustalColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void zappoColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
- {\r
+ protected void taylorColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
- {\r
+ protected void helixColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void strandColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
+ protected void turnColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void buriedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
- {\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void PIDColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void font_actionPerformed(ActionEvent e)\r
- {\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
- {\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void printMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
- {\r
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void findMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
+ }\r
\r
- protected void jpred_actionPerformed(ActionEvent e)\r
- {\r
+ protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void deleteGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
+ protected void copy_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void cut_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
+ protected void delete_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void pasteNew_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
+ protected void pasteThis_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
- {\r
+ protected void createPNG_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void font_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
- {\r
+ protected void fullSeqId_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void epsFile_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void jpred_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ protected void scaleAbove_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void scaleLeft_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void inputText_actionPerformed(ActionEvent e) {\r
+ protected void scaleRight_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void modifyPID_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
+ protected void modifyConservation_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void preferences_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- protected void about_actionPerformed(ActionEvent e) {\r
+ protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
+ }\r
\r
- }\r
+ protected void inputText_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void documentation_actionPerformed(ActionEvent e) {\r
+ }\r
\r
+ protected void about_actionPerformed(ActionEvent e) {\r
+ }\r
}\r
-\r
git://source.jalview.org / jalview.git / blobdiff